Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_043772194.1 U743_RS13275 ROK family protein
Query= reanno::SB2B:6937235 (310 letters) >NCBI__GCF_000733765.1:WP_043772194.1 Length = 308 Score = 274 bits (700), Expect = 2e-78 Identities = 149/299 (49%), Positives = 190/299 (63%), Gaps = 4/299 (1%) Query: 2 YRSGIDLGGTKIELVTLNEKGEEVFRKRVPTPK-DYRATLEAVAGLVHDSEKETGQVS-S 59 YR G+DLGGTKIE+ L+ +GE V R+R TP DY A + V +V E+E G Sbjct: 5 YRIGVDLGGTKIEVALLDAEGEFVARRREATPVGDYGAIIRQVREMVTAVEREQGLTGVP 64 Query: 60 VGIGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGG 119 VG G PG VS TGR+KNSN+V LN Q + +DL A LGREVRIANDA+CFA+SE+ DG Sbjct: 65 VGAGTPGAVSRATGRMKNSNSVCLNDQMLREDLMAALGREVRIANDADCFALSEATDGAA 124 Query: 120 AGKTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTAD--EFNSTRCFCGN 177 AG VFG ILGTG G G+ ++ ++ G N I GEWGHNPLPW + E + + G Sbjct: 125 AGGGTVFGVILGTGVGGGVVVDGRLLAGPNAIAGEWGHNPLPWPRPEWNEVPGPKGWDGR 184 Query: 178 ADCIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVI 237 IET+ G G + D GG+A + I A G+ A A R+ DRLARALA ++ Sbjct: 185 YGSIETWCCGPGLLADHERSGGQAENAQAICAAAEAGDHQAMATLARWEDRLARALASIV 244 Query: 238 NLLDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLW 296 N+LDP+VIV+GGG+S ID +Y ++PAL ++V TK+V G SSGVRGAAWLW Sbjct: 245 NILDPEVIVVGGGLSGIDRMYRHVPALWTEWVFSDRVDTKLVPARFGDSSGVRGAAWLW 303 Lambda K H 0.318 0.138 0.424 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 327 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 310 Length of database: 308 Length adjustment: 27 Effective length of query: 283 Effective length of database: 281 Effective search space: 79523 Effective search space used: 79523 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory